OCA at 11:46, 1 February 2024

OCA — Thu, 01 Feb 2024 11:46:22 GMT

←Older revision		Revision as of 11:46, 1 February 2024
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8re3 is ~~ON HOLD~~	+	==Crystal Structure determination of Dye-decolorizing Peroxidase (DyP) mutant M190G from Deinoccoccus radiodurans==
		+	<StructureSection load='8re3' size='340' side='right'caption='[[8re3]], [[Resolution\|resolution]] 1.51Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8re3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RE3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8RE3 FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.51Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8re3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8re3 OCA], [https://pdbe.org/8re3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8re3 RCSB], [https://www.ebi.ac.uk/pdbsum/8re3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8re3 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9RZ08_DEIRA Q9RZ08_DEIRA]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dye-decolorizing peroxidases (DyPs) are heme proteins with distinct structural properties and substrate specificities compared to classical peroxidases. Here, we demonstrate that DyP from the extremely radiation-resistant bacterium Deinococcus radiodurans is, like some other homologues, inactive at physiological pH. Resonance Raman (RR) spectroscopy confirms that the heme is in a six-coordinated-low-spin (6cLS) state at pH 7.5 and is thus unable to bind hydrogen peroxide. At pH 4.0, the RR spectra of the enzyme reveal the co-existence of high-spin and low-spin heme states, which corroborates catalytic activity towards H(2)O(2) detected at lower pH. A sequence alignment with other DyPs reveals that DrDyP possesses a Methionine residue in position five in the highly conserved GXXDG motif. To analyze whether the presence of the Methionine is responsible for the lack of activity at high pH, this residue is substituted with a Glycine. UV-vis and RR spectroscopies reveal that the resulting DrDyPM190G is also in a 6cLS spin state at pH 7.5, and thus the Methionine does not affect the activity of the protein. The crystal structures of DrDyP and DrDyPM190G, determined to 2.20 and 1.53 A resolution, respectively, nevertheless reveal interesting insights. The high-resolution structure of DrDyPM190G, obtained at pH 8.5, shows that one hydroxyl group and one water molecule are within hydrogen bonding distance to the heme and the catalytic Asparagine and Arginine. This strong ligand most likely prevents the binding of the H(2)O(2) substrate, reinforcing questions about physiological substrates of this and other DyPs, and about the possible events that can trigger the removal of the hydroxyl group conferring catalytic activity to DrDyP.

-	~~Authors: Salgueiro~~, ~~B.A~~., Frade, K., ~~Frazao~~, C., ~~Matias~~, P., ~~Moe~~, E.	+	Biochemical, Biophysical, and Structural Analysis of an Unusual DyP from the Extremophile Deinococcus radiodurans.,Frade K, Silveira CM, Salgueiro BA, Mendes S, Martins LO, Frazao C, Todorovic S, Moe E Molecules. 2024 Jan 11;29(2):358. doi: 10.3390/molecules29020358. PMID:38257271<ref>PMID:38257271</ref>

-	~~Description: Crystal Structure determination~~ of ~~Dye~~-~~decolorizing Peroxidase (DyP) mutant M190G from Deinoccoccus~~ radiodurans	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Frade, K]]	+	<div class="pdbe-citations 8re3" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Moe, E~~]]	+	== References ==
-	[[Category: Matias, P]]	+	<references/>
-	[[Category: ~~Salgueiro, B.A~~]]	+	__TOC__
-	[[Category: ~~Frazao, C~~]]	+	</StructureSection>
		+	[[Category: Deinococcus radiodurans]]
		+	[[Category: Large Structures]]
		+	[[Category: Frade K]]
		+	[[Category: Frazao C]]
		+	[[Category: Matias P]]
		+	[[Category: Moe E]]
		+	[[Category: Salgueiro BA]]

OCA at 22:05, 27 December 2023

OCA — Wed, 27 Dec 2023 22:05:32 GMT

←Older revision		Revision as of 22:05, 27 December 2023
Line 3:		Line 3:
	The entry 8re3 is ON HOLD		The entry 8re3 is ON HOLD

-	Authors: Salgueiro, B. A., Frade, K., Frazao, C., Matias, P., Moe, E.	+	Authors: Salgueiro, B.A., Frade, K., Frazao, C., Matias, P., Moe, E.

	Description: Crystal Structure determination of Dye-decolorizing Peroxidase (DyP) mutant M190G from Deinoccoccus radiodurans		Description: Crystal Structure determination of Dye-decolorizing Peroxidase (DyP) mutant M190G from Deinoccoccus radiodurans
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Frade, K]]
	[[Category: Moe, E]]		[[Category: Moe, E]]
	[[Category: Matias, P]]		[[Category: Matias, P]]
-	[[Category: Salgueiro, B. A]]	+	[[Category: Salgueiro, B.A]]
	[[Category: Frazao, C]]		[[Category: Frazao, C]]
-	[[Category: Frade, K]]

OCA: Protected "8re3" [edit=sysop:move=sysop]

OCA — Wed, 20 Dec 2023 08:49:42 GMT

Protected "8re3" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:49, 20 December 2023

OCA: New page: '''Unreleased structure''' The entry 8re3 is ON HOLD Authors: Salgueiro, B. A., Frade, K., Frazao, C., Matias, P., Moe, E. Description: Crystal Structure determination of Dye-decoloriz...

OCA — Wed, 20 Dec 2023 08:49:41 GMT

New page: '''Unreleased structure''' The entry 8re3 is ON HOLD Authors: Salgueiro, B. A., Frade, K., Frazao, C., Matias, P., Moe, E. Description: Crystal Structure determination of Dye-decoloriz...

New page

'''Unreleased structure'''

The entry 8re3 is ON HOLD

Authors: Salgueiro, B. A., Frade, K., Frazao, C., Matias, P., Moe, E.

Description: Crystal Structure determination of Dye-decolorizing Peroxidase (DyP) mutant M190G from Deinoccoccus radiodurans
[[Category: Unreleased Structures]]
[[Category: Moe, E]]
[[Category: Matias, P]]
[[Category: Salgueiro, B. A]]
[[Category: Frazao, C]]
[[Category: Frade, K]]

8re3 - Revision history

OCA at 11:46, 1 February 2024

OCA at 22:05, 27 December 2023

OCA: Protected "8re3" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8re3 is ON HOLD Authors: Salgueiro, B. A., Frade, K., Frazao, C., Matias, P., Moe, E. Description: Crystal Structure determination of Dye-decoloriz...